TBL3

transducin beta like 3, the group of WD repeat domain containing|UTPb subcomplex

Basic information

Region (hg38): 16:1972053-1982929

Links

ENSG00000183751 ∙ NCBI:10607 ∙ OMIM:605915 ∙ HGNC:11587 ∙ Uniprot:Q12788 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TBL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBL3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	2	5
missense			84	6		90
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			38	4		42
Total	0	0	122	13	2

Variants in TBL3

This is a list of pathogenic ClinVar variants found in the TBL3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-1972177-G-T		not specified	Uncertain significance (Mar 16, 2022)
16-1972204-A-G		not specified	Uncertain significance (Nov 26, 2024)
16-1974096-G-A		not specified	Uncertain significance (Oct 24, 2024)
16-1974200-G-A		not specified	Uncertain significance (Mar 08, 2024)
16-1974204-A-G		not specified	Uncertain significance (Nov 08, 2022)
16-1974227-G-A		not specified	Likely benign (Sep 07, 2022)
16-1974264-C-T		not specified	Uncertain significance (Sep 26, 2024)
16-1974398-C-T		not specified	Uncertain significance (Aug 26, 2022)
16-1974413-C-T		not specified	Uncertain significance (Nov 10, 2022)
16-1974557-G-A		not specified	Uncertain significance (Dec 22, 2023)
16-1974558-G-A			Benign (Feb 20, 2018)
16-1974580-G-A		not specified	Uncertain significance (Sep 01, 2021)
16-1974596-G-C		not specified	Uncertain significance (Oct 16, 2023)
16-1974596-G-T		not specified	Uncertain significance (Apr 05, 2023)
16-1974614-A-G		not specified	Uncertain significance (Sep 27, 2024)
16-1974616-G-A		not specified	Uncertain significance (Sep 28, 2022)
16-1974617-C-T		not specified	Uncertain significance (Feb 15, 2023)
16-1974631-C-T		not specified	Uncertain significance (Mar 23, 2022)
16-1974634-G-A		not specified	Uncertain significance (Aug 02, 2023)
16-1974656-C-T		not specified	Uncertain significance (Dec 12, 2023)
16-1974774-G-A		not specified	Uncertain significance (Oct 26, 2022)
16-1974783-C-T		not specified	Uncertain significance (May 27, 2022)
16-1974810-G-A		not specified	Uncertain significance (Nov 07, 2023)
16-1974832-C-T		not specified	Uncertain significance (Oct 18, 2021)
16-1974843-G-C		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBL3	protein_coding	protein_coding	ENST00000568546	22	10897

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.41e-11	0.999	125688	0	55	125743	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.206	540	527	1.03	0.0000364	5152
Missense in Polyphen		143	166.68	0.85794		1746
Synonymous	-2.42	286	238	1.20	0.0000178	1682
Loss of Function	2.97	24	45.6	0.526	0.00000222	469

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000699	0.000693
European (Non-Finnish)	0.000242	0.000237
Middle Eastern	0.000218	0.000217
South Asian	0.000230	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.681
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.08

Haploinsufficiency Scores

• pHI: 0.162
• hipred: Y
• hipred_score: 0.690
• ghis: 0.520

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.957

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tbl3

Zebrafish Information Network

• Gene name: tbl3
• Affected structure: T cell
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);rRNA processing
• Cellular component: nucleus;nucleoplasm;nucleolus;small-subunit processome;Pwp2p-containing subcomplex of 90S preribosome
• Molecular function: RNA binding;protein binding